Bioinformatics Analysis of DGAT1 Gene in Domestic Ruminnants

Bioinformatics Analysis of DGAT1 Gene in Domestic Ruminnants SIROUS EIDIVANDI Abstract Diacylglycerol-O-acyltransferase (DGAT1) gene encodes diacylglyceroltransferase enzyme that playsan important role in glycerol lipid metabolism. DGAT1 is considered to be the key enzyme in controlling the synthesis of triglycerides in adipocytes. This enzyme catalyzes the final step of triglyceride synthesis (transform triacylglycerol (DAG) into triacylglycerol (TAG). A total of 20 DGAT1 (8,9 Exones) gene sequences belonging to 5 species include cattle (Bos Taurus and BosIndicus), Goats, Sheep and Buffalo were analyzed, and the differentiation within and among the species was also studied. The length of the Exone 8 and Exone 9 respectively were 75bp and 64bp (total: 139bp). Observed genetic diversity was higher among species than within species, and Bos Taurus had more polymorphisms than any other species. Novel amino acid variation sites were detected within several species which might be used to illustrate the functional variation. Differentiation of the DGAT1 gene was obvious among species, and the clustering result was consistent with the taxonomy in the National Center for Biotechnology Information. Keywords: DGAT1gene, Bioinformatic, Ruminnants Introduction Bioinformatics has become an important part of many areas of biology. In experimental molecular biology, bioinformatics techniques such as image and  signal processing  allow extraction of useful results from large amounts of raw data. In the field of genetics and genomics, it aids in sequencing and annotating genomes and therefore we can observe polymorphic sites, Gene Expressions,Similarities and differences between and within gene sequences in the varies Species and etc. on the other hands gene mapping research has led to the discovery of many polymorphic sites throughout the Ruminants genome that can serve as genetic markers for selection in breeding schemes (Jing-Fen K.et al., 2008). Diacylglycerolacyltransferases (DGATs) are involved in the process of catalyzation of the final step of the triacylglycerol (TAG) biosynthesis (Hatzopoulos et al., 2011). This enzyme has been found to be encoded by two genes (DGAT1 and DGAT2 ), of which the most studied and important one reavealed to be DGAT1 . This gene is responsible for the codification of the protein related to DGATs activity (Cases et al., 2001). In bovine, this gene is located on the centromeric end of the bovine chromosome 14 (BTA14), harboring the QTL with a large impact on milk production traits (Grisart et al.,2002; Winter et al., 2002). DGAT1is a microsomal enzyme catalyzing the addition of fatty acyl Co A to 1, 2, diacylglycerol to yield CoA plus triglycerol and is important in lipogenesis in many tissues, including mammary gland (Kuhnet al.1998). DGAT1 gene is considered to be a very strong positional candidate gene for fat percent of milk. Kaupeet al., 2004 reported the frequency of this substitution in various cattle breeds and grouped them from very low frequency to fixation inBosindicuscattle breeds. DGAT1 gene is considered to be a very strong positional candidate gene for fat percent of milk. Kaupeet al. [2004] studied Polymorphism of this gene in Bostaurus and Bosindicus breeds. They claimed that K allele of DGAT1 gene is a wild type and the A allele substitution probably occurred after the divergence of Bostaurus and Bosindicus (Kaupeet al., 2004). Recently, many studies showed a significant association between polymorphism of this gene and milk production traits (Grisartet al., 2002; Kharrati Koopaeiet al., 2012; Ripoli MV et al., 2006). There is a general consensus in the literature that the alanine to lysine amino acid change (K232A) in exon 8 of the DGAT1 gene is associated with reduced milk production (Spelman et al ., 2002; Thaller et al ., 2003a; Banos et al., 2008), Materials and Methods A total of 20 sequences with Exons of the DGAT 1 gene and the amino acid sequences belonging to 5 species were obtained from GenBank (Table 1). All the sequences were aligned using the Clustal Omega program implemented in EMBL-EBI service. DnaSP (version 5.1) software was used to analyze the haplotype diversity (Hd), the average number of nucleotide differences (Tajima 1983), the  nucleotide diversity (p), synonymous nucleotide diversity (ps), nonsynonymousnucleotide diversity (pa) with the Jukes and Cantor correction, the polymorphic site(S), the singleton variable sites (SP), and the parsimony informative sites (PIP) for each species, and the average number of nucleotide substitutions per site between species (Dxy) (Lynch and Crease, 1990). The phylogenetic tree among 5 species based on the D xy was constructed using the unweight pair group method with the arithmetic mean (UPGMA) implemented in Mega 6 software. Table 1: DGAT1 gene, Exons 8 and 9 sequences of 5 species Results and Discussion DGAT1 gene, Exon 8, The Exon sequence of 8 has 75bp in domestic ruminants. We used 6,4,4,4 and 2 sequences of the exon respectively in BosTaurus, Bosindicus, Bubalusbubalis, Ovisaries and Capra hircus(table 1). DnaSP (version 5.1) software was used to analysis of them. The haplotype diversity (Hd) within the sequences of sheep, goat and buffalo was 0, because there wasn’t any polymorphism in these sequences. The haplotype diversity (Hd) within the sequences of bostaurus and bosindicus were shown respectively, 0.733 and 0.5 with 3 and 2 polymorphic sites. DGAT1 gene, Exon 9, The Exon sequence of 9 has 64bp in domestic ruminants.The haplotype diversity (Hd) within the sequences of goatbostaurus and bosindicus was 0 but the haplotype diversity (Hd) within the sequences of sheep and Buffalo was 0.5 with 2 polymorphic sites. Polymorphism and Genetic Diversity among Species The alignment of 20 sequences of 8 and 9 exons within the region of 139bp and containing gapswas carried out using BioEdit. The results of DnaSP analysis indicated that theselected region (1–140) of the 20 sequences from different species have 139sites, excluding sites with gaps (2). There are 134 invariable (monomorphic) sites and 4 variable (polymorphic) sites that include 3 singleton variable sites and 1 parsimonyinformative sites.The nucleotide diversity (p = 0.00885) and the average number  of nucleotide differences ( K = 1.221) for all sequences are lower than the highest values in bostaurus (p = 0.01014 ,K = 1.4). The polymorphic information and haplotype diversity of the DGAT1 gene (8 and 9Exons) for each species are listed in Table 2. Table 2: Genetic diversity of the DGAT1gene(8 and 9Exons) in 5 species h, Number of haplotypes; H d, haplotype diversity; K, average number of nucleotide differences; Ï€, Nucleotide diversityÏ€s, synonymous nucleotide diversity; Ï€a, nonsynonymous nucleotide diversity; S, Number of polymorphic sites; SP, singleton variable sites; PIP, parsimony informative sites. The most variable sites (3), singleton variable sites (2), and average number of nucleotide differences (1.4) were found in bostaurus, whichshowed that bostaurus had the highest genetic diversity. Usually, more genetic diversity is most useful for natural selection. The higher genetic diversity of the DGAT1 gene in bostaurus might be related to its extensive adaptability and survival for a polyembryonic animal (Jing-Fen K.et al., 2008). Amino Acid Variation and Genetic Effects Higher polymorphism was observed among species than within species, after the 20complete amino acid sequences were aligned using the Clustal Omega program implemented in BioEdit software. The stop codons in thesequences of the exon 8, 9in Ovisaries, Capra hircus, bosindicus and Bubalus bubalisare onlyUGA but in bos Taurus there are UGA and UAA.Also the exons of bos Taurus had CAC that code histidine and this codone was shown in the other species. The differences between Bos Taurus and the other species in this study maybe related to difference effects of the DGAT 1 gene one the milk production traits. There is a general consensus in the literature that the alanine to lysine amino acid change (K232A) in exon 8 of the DGAT1 gene is associated with reduced milk production (Spelman et al, 2002; Thaller et al, 2003a; Banos et al, 2008), DNA Divergence and Clustering Analysis The average number of nucleotide substitutions per site (Dxy) of the DGAT1 gene between species is shown in Table3. Dxyis the index of DNA divergence between or among the sequences. The larger D xy has the smaller the genetic distance. Based on Dxy, a phylogenetic tree was constructed for all the species using the UPGMA method (Fig.1). The divergence time among different species was also labeled on the scale bar calculated from the average nonsynonymous nucleotide rate(0.85 9 10 – 9per year, Li and Dan1991). The dendrogram of different species based on the differentiation of the DGAT1gene agreed with the taxonomy of NCBI. The smallest D xy(0.0000) and divergence showed the closest relationship between Sheep and Goat, which basically accords with that of Yang and Yoder ( 2003) and Wildman et al. (2003). The largest D xy(0.0146) and divergence time displayed the earliest differentiation between BosTaurus and Buffalo, Sheep and Goat, with the average value of 0.0087 for all speci es(Table 3, Fig1). Table 3: Average nucleotide substitution per site(Dxy) Fig. 1 Phylogenetic tree of the DGAT1(8,9 Exone)gene among 5 species References Banos, G., Woolliams, J.A., Woodward, B.W., Forbes,A.B. and Coffey, M.P. (2008) Impact of singlenucleotide polymorphisms in Leptin, LeptinReceptor, Growth Hormone Receptor, andDiacylglycerolAcyltransferase (DGAT1) geneloci on milk production, feed, and body energytraits of UK dairy cows. Journal of Dairy Science91: 3190–3200. Cases S, Smith SJ, Zheng YW, Myers HM, Lear SR, Sande E, Novak S, Collins C, Welch CB, Lusis AJ,et al.(1998) Identification of a gene encoding an acyl CoA:diacylglycerolacyltransferase, a key enzyme in triacylglycerol synthesis. ProcNatlAcadSci USA 95:13018-13023 Cases S, Stone SJ, Zhou P, Yen E, Tow B, Lardizabal KD, Voelker T, Farese RV (2001). Cloning of DGAT2, a second mammalian diacylglycerolacyltransferase and related family members. Journal of Biological Chemistry 276:38870–38876. Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R. .( 2002) Positional candidate cloning of a QTL in dairy cattle: Identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition.Genome Research.12, 222-231. Grisart B, Farnir F, Karim L, Cambisano N, Kim J, Kvasz A, Mni M, Simori P, Frere J, Coppieters W,et al.(2004) Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. ProcNatlAcadSci USA 101:2308-2403 Jing-Fen K., Xiang-Long L., Rong-Yan Z., Lan-Hui L., Fu-Jun F. and Xiu-Li G.(2008)Bioinformatics Analysis of Lactoferrin Gene for SeveralSpecies.Biochem Genet 46:312–322 Kaupe B, Winter A, Fries R and Erhardt G (2004) DGAT1 polymorphism inBosIndicusandBostauruscattle breeds. J Dairy Res 71:182-187. KharratiKoopaei H, Mohammad Abadi MR, Ansari Mahyari S, EsmailizadehKoshkoiyeh A,Tarang AR, Potki P. (2012) Effect of DGAT1 variants on milk composition traits in Iranian Holstein cattlepopulation. Animal Science Papers and Reports. 3, 231-239. Kuhn CH, Thaller G, Winter A, Bininda-Emonds O, Kaupe B, Erhardt G, Bennewitz J, Schwerin M and Fries R (2004) Evidence for multiple alleles at the DGAT1 locus better explains a quantitative trait locus with major effect on milk fat content in cattle. Genetics 167:1873-1881. Ripoli MV, Corva P, Giovambattita G. (2006) Analysis of a polymorphism in the DGAT1 gene in 14 cattlebreeds through PCR-SSCP methods. Research Veterinary Science. 80, 287-290 Smith SJ, Cases S, Jensen DR, Chen HC, Sande E, Tow B, Sanan DA, Raber J, Eckel RH and FareseJr RV (2000) Obesity resistance and multiple mechanisms of triglyceride synthesis in mice lacking Dgat. Nat Genet 25:87-90. Spelman RJ, Ford CA, McElhinney P, Gregory GC and Snell RG (2002) Characterization of the DGAT1 gene in the New Zealand dairy population. J Dairy Sci 85:3514-3517. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:  437–460 Thaller G, Kuhn C, Winter A, Ewlad G, Bellmann O, Wegner J, Zuhlke H and Fries R (2003) DGAT1, a new positional and functional candidate gene for intramuscular fat deposition in cattle. Anim Genet 34:354-357. Winter A, Kramer W, Werner F, Kollers S, Kata S, Durstewitz G, Buitkamp J, Womack W, Thaller G and Fries R (2002) Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA:diacylglycerolacyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. ProcNatlAcadSci USA 99:9300-9305.

Byzantine Civilization

Byzantine Civilization began â€Å"by the end of 3rd century A. D. † or 330 A. D. to be more exact (Byzantine.. n. p. ). Byzantine Civilization entails â€Å"works of art considered an expressionist interpretation of late Roman art† (Byzantine.. n. p. ). Significance of San Vitale, Ravenna San Vitale is very significant because until today it is still intact (Byzantine.. n. p. ). Aside from that, it reiterates the accomplishments of Emperor Justinian who played a major role in the â€Å"First Byzantine Golden Age† (Byzantine.. n. p.).Significance of Hagia Sophia, Istanbul Hagia Sophia which is located in Istanbul is a church created by Constantine (Byzantine.. n. p. ). It has been restored several times during the period of Byzantine Civilization (Byzantine.. n. p. ). Hagia Sophia has been very significant as it is the â€Å"most important monuments of the Byzantine Architecture† (Byzantine.. n. p. ). This extremely important landmark has a garden that sur rounds the basilica and is composed of a hall, central room, as well as, a gallery (Byzantine.. n. p. ).Furthermore, it is exceedingly large; in fact, it comes next to St. Peters, Duomo, and St. Pauls, thus making it the fourth largest church (Byzantine.. n. p. ). Significance of St. Mark’s, Venice St. Mark’s basilica is significant because this has been the shrine designed exclusively for the purpose of keeping the saint’s bones (Byzantine.. n. p. ). Even though it caught fire before, the architects of the Byzantine period was able to successfully restore it making it eventually as one of the best monuments of Byzantine Civilization (Byzantine..n. p. ). In addition to that, it contributed greatly to civilization since its location is very strategic (Byzantine.. n. p. ). This is evidenced by â€Å"Venice’s unsurpassed position in trade with the East† (Byzantine.. n. p. ). References Byzantine Civilization. 2005. n. a. 11 August 2007 http://www. foc usmm. com/civi_021. htm The Columbia Encyclopedia. Byzantine Civilization. New York: Columbia University Press, 2005.

Fairytales are not what they seem. Essay - 1243 Words

INTRO Sex. Pure unadulterated sex. When we think of sex, it is not usually in the context of a fairytale. Fairytales are for children, virgin ears. Over the years, fairytales have been â€Å"cleaned up† for young ears- we have become accustomed to the bland Disney versions of tales. How many of us can recount a version separate from the animated classics of our childhood? It is truly hard to believe that sometimes there are much more racy versions of these same tales. Today, I ‘d like to share one such variation of Little Red Riding Hood called In the Company of Wolves, written by Angela Carter. I will recount ancient folklore of werewolves, introduce the sexually charged characters as I walk with you through the seemingly familiar yet much†¦show more content†¦She has been loved too much to know how to be scared. It was the middle of winter, and the silence of the woods seemed to close down upon our heroine like a pair of jaws. Suddenly she heard a distant howl of a wolf, and she sprang to the handle of a well-concealed knife, but nobody was there. Suddenly, a clamor among the bushed produced a fully clothed and very handsome young man holding a very large rifle. They walked along the worn path for some time together laughing like old friends. It was only a mere half-mile to go till the warmth and safety of her grandmother’s house when the dashing young stranger proposed a bet. He insisted that with the help of a compass, he would surely make it to the grandmother’s house before she would on the path. A game was made of it, and if he won, he was to have a kiss. At the mention of the kiss, Little Red lowered her eyes and blushed, commonplace of rustic seduction. Although it was getting dark, she wanted to dawdle on her way so that the handsome gentleman would win his wager. She f orgot to be afraid of the beasts. TR*: It was this wager that was to signal the end of innocence for our young heroine. 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Things a Successful School Principal Does Differently

Being a principal has its challenges. It is not an easy profession. It is a high-stress job that most people are not equipped to handle. A principal’s job description is broad. They have their hands in virtually everything related to students, teachers, and parents. They are the chief decision-maker in the building. A successful school principal does things differently. As with any other profession, there are those principals who excel at what they do and those who lack the skills necessary to be successful. Most principals are in the middle of that range. The best principals have a particular mindset and a leadership philosophy that allows them to be successful. They utilize a combination of strategies that make themselves and others around them better thus allowing them to be successful. Surround Themselves with Good Teachers Hiring good teachers makes a principal’s job easier in virtually every aspect. Good teachers are solid disciplinarians, they communicate well with parents, and they provide their students with a quality education. Each of these things makes a principal’s job easier. As a principal, you want a building full of teachers that you know are doing their job. You want teachers that are 100% committed to being effective teachers in every aspect. You want teachers who not only do their job well but are willing to go above and beyond the core requirements to ensure that every student is successful. Simply put, surrounding yourself with good teachers makes you look better, makes your job easier, and allows you to manage other aspects of your job. Lead by Example As a principal, you are the leader of the building. Every person in the building is watching how you go about your daily business. Build a reputation for being the hardest worker in your building. You should almost always be the first one to arrive and the last one to leave. It is essential that others know how much you love your job. Keep a smile on your face, maintain a positive attitude, and handle adversity with grit and perseverance. Always maintain professionalism. Be respectful to everyone and embrace differences. Be the model for fundamental qualities such as organization, efficiency, and communication. Think Outside the Box Never put limitations on yourself and your teachers. Be resourceful and find creative ways to meet needs when issues arise. Do not be afraid to think outside the box. Encourage your teachers to do the same. Successful school principals are elite problem solvers. Answers do not always come easy.  You have to utilize the resources creatively you have or figure out ways to get new resources to meet your needs. A terrific problem solver never dismisses another person’s idea or suggestion. Instead, they seek out and value input from others cooperatively creating solutions to problems. Work With People As a principal, you have to learn to work with all different types of people. Each person has their own personality, and you must learn to work effectively with each type. The best principals are able to read people well, figure out what motivates them, and strategically plant seeds that will eventually blossom into success. Principals must work with every stakeholder in the community. They should be skilled listeners who value feedback and use it to make recognizable changes. Principals should be on the front lines, working with the stakeholders to improve both their community and school. Delegate Appropriately Being a principal can be overwhelming. This is often amplified as principals by nature are typically control freaks. They have high expectations on how things should be done making it difficult to let others take the lead role. Successful principals are able to get past this because they realize there is value in delegating. First of all, it shifts the burden of responsibility from you, freeing you up to work on other projects. Next, you can strategically make individuals responsible for projects that you know fit their strengths and will help build their confidence. Finally, delegating reduces your overall workload, which in turn keeps your stress level at a minimum. Create and Enforce Proactive Policies Every principal should be an adept policy writer. Each school is different and has their own unique needs in terms of policy. Policy works best when it is written and enforced in such a way that very few want to take the chance to receive the attached consequences. Most principals will spend a large part of their day dealing with student discipline. Policy should be seen as a deterrent to distractions that interrupt learning. Successful principals are proactive in their approach to policy writing and student discipline. They recognize potential problems and address them before they become a significant issue. Look for Long-Term Solutions to Problems A quick fix is seldom the right solution. Long-term solutions require more time and effort in the beginning. However, they typically save you time in the long run, because you won’t have to deal with it as much in the future. Successful principals think two to three steps ahead. They address the little picture by fixing the large picture. They look beyond the specific circumstance to get to the cause of the problem.  They understand that taking care of the core problem may head off several smaller issues down the road, potentially saving both time and money. Become an Information Hub Principals have to experts in many different areas including content and policy. Successful principals are a wealth of information. They stay up-to-date on the latest educational research, technology, and trends. Principals should at least have a working knowledge of the content being taught in each grade for which they are responsible. They follow educational policy at both the state and locals areas. They keep their teachers informed and are able to offer tips and strategies concerning best classroom practices. Teachers respect principals who understand the content they are teaching. They appreciate when their principal offers well thought out, applicable solutions to problems they may be having in the classroom. Maintain Accessibility As a principal, it is easy to get so busy that you shut your office door to try and get a few things done. This is perfectly acceptable as long as it isn’t done a regular basis. Principals must be accessible to all stakeholders including teachers, staff members, parents, and especially students. Every principal should have an open door policy. Successful principals understand that building and maintaining healthy relationships with everyone you work with is a key component to having an outstanding school. Being in high demand comes with the job. Everyone will come to you when they need something or when there is a problem. Always make yourself available, be a good listener, and most importantly follow through on a solution. Students are the First Priority Successful principals keep students as their number one priority. They never deviate from that path. All expectations and actions are directed to ensure a quality school for better students both individually and as a whole. Student safety, health, and academic growth are our most fundamental duties. Every decision that is made has to take the impact it will make on a student or group of students into account. We are there to nurture, counsel, discipline, and educate each and every student. As a principal, you must never lose sight of the fact that students should always be our focal point.